##################
##              ##
## Introduction ##
##              ##
##################

Welcome to libngs, the Nifty GNU Sequence Library (or Next Generation
Sequencing Library, whatever).

This library was and accompanying tools were originally written to handle whole
genome bisulfite sequencing data generated with the Illumina technology.  Since
then it has been found useful in a few other situations, especially when
preparing sequences for de-novo assembly (quality trimming, adaptors clipping,
removal of clonal reads, etc).

###################
##               ##
## Prerequisites ##
##               ##
###################

1) flex

To compile libngs and its tools you will need flex (the Fast Lexical Analyser).
In most Linux distributions, this comes in the `flex' package.
For more information, see http://flex.sourceforge.net/

2) libglib

You will need libglib and its header files in a version greater or equal to
2.16.  On a Debian system, this can be found in the libglib2.0-0 and
libglib2.0-0-dev packages.  Other distributions probably use similar names.
For more information see http://www.gtk.org/

##################
##              ##
## Installation ##
##              ##
##################

For details see the accompanying install file. In brief:

For a system-wide installation:

./configure
make
sudo make install

For a user-specific installation:

./configure --prefix=/somewhere/where/you/have/write/access
make install

####################
##                ##
## What's inside? ##
##                ##
####################

libngs itself (in the src/libngs/ directory) has various parsing functions, and
structures to hold sequences and mapping informations.  It also has function to
manipulate these structures in various ways.

The tools that come with libngs (in the src/bin/ directory) allow various type
of manipulations on sequence data files, and mapping data.  If you understand
the name of the tool, then it probably does what you think. If you don't, then
you probably don't need it.  In doubt try:
< whatever tool name> -h

Also, a summary description of the tools can be found in the manual, located on
the `doc' directory.

In general, the tools are designed to be chained together and read from stdin.
For instance:

bzcat infile.bz2 |  fastq_sample -n 50 - | fastq_trim -q 10 - | gzip -c - > outfile.gz

This decompresses infile.bz2, randomly samples 50 of the resulting sequences,
quality trim the sequences and compresses the resulting file with gzip.  The
tools might need some extra options, but you get the idea.

There are also a few helper scripts in src/scripts/ that might be useful.

# vim:spell: